Octopus itself is designed to perform a 0-downtime deployment process, but there are times when you do need to stop or start an IIS application pool. Thankfully, for these occasions, there is a set of community step templates available for manipulating the AppPool.
To find these, navigate to Library -> Step Templates -> Browse Library, and then search for AppPool - you should find steps to Stop, Start, and Restart (as well as some other actions).
Once you have installed these, you can add them to your deployment process with Add Step then adding the step that you would like (IIS AppPool - Stop etc).
From there, add your target machine roles, Application pool by name, and any other settings you wish, then hit Save, Create a release, and deploy it.
Hope this helps! Please don’t hesitate to let us know if you have any further questions.